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For Pakistan's powerful military, the unprecedented floods have been a mixed blessing. The military has won plaudits for leading the rescue and relief efforts, as the civilian government was criticized as being impassive. But with 72,000 soldiers involved across the country, the disaster has strained resources to the point where troops have been diverted from holding crucial territory that has been wrenched back from the Pakistani Taliban, and future offensives have been put on hold.

In some of the worst hit areas of southern Punjab and Sindh, the army merely needed to deploy non-combat troops who were garrisoned nearby. "In the northern part, where the troops were engaged in operations against the militants, there the units  in part or whole  have been forced to take part in the rescue and relief efforts," says a senior military official who has requested anonymity. That includes the Swat Valley, where a major offensive last year chastened the Pakistani Taliban, who had terrorized its population for two years. "The present deployment was to prevent against the return of the militants." (See the aftermath of the floods.)

The military official acknowledges that there is reason to worry that the distraction of the floods could open up a vacuum that could be filled by the militants. "It's not a misplaced fear," he says. The scale of disaster has already brought a resigned acceptance of the militants' role in the relief efforts. "[Given] the kind of catastrophe that you see, you have to work with the devil," the military official says. "One would like to offer him space to help us." The most prominent example has been the Jamaat-ud-Dawa, a proscribed terror outfit blamed for the November 2008 Mumbai massacre, which has reemerged under the new name Falah-e-Insaniat Foundation to set up camps that offer food, shelter and medicine. The government insists that the group operates only a fraction of the camps, but the group has acquired an unsettling confidence. Nawai-Waqt, a widely read Urdu daily, carried an advertisement from Jamaat-ud-Dawa on Sept. 4, signed by its controversial leader Hafiz Saeed Muhammad, appealing for more funding for the flood efforts.

The army says it is well aware of the threat in militarily sensitive flood-affected areas like Swat. "We are taking all the safeguards not to allow the militants to reenter," says the military official. "In Swat, the units are on guard." There is also a concern that in other parts of the badly hit northwest and southern Punjab, where militants continue to have considerable influence, new recruits could be attracted. "If, when the people go back, the state fails to provide basic means of survival, then they could be lured by the militants."

For the moment, where the fighting continues in the tribal areas, the military is losing its edge to the tactical difficulties the floods present. In Khyber, Bajaur and particularly Orakzai, heavy airpower is still being used in tandem with troops on the ground. "Orakazai was a stronghold of Hakimullah Mehsud," the official says, referring to the fugitive leader of the Pakistani Taliban. "When they were dislodged from South Waziristan, the whole gang had gathered in Orakzai and North Waziristan." But the floods now mean that the army is unlikely to be able to pursue the militants into North Waziristan, as even Secretary of Defense Robert Gates acknowledged last week. "In the areas where one had a plan for an offensive position, one is being forced to take a defensive positions," says the military official. Washington has long been urging Pakistan to take action in the tribal agency, where the Haqqani network and other elements that comprise the most potent threat to U.S. and NATO troops across the border are based. In the absence of a Pakistani offensive, there has been an intensification of CIA-operated drone strikes targeting the Haqqani network there. Over the past week, there have been seven such strikes; three fired on Sept. 8 killed 14 suspected militants.

For many months, as Islamabad said that its resources were too stretched to act, Pakistani reluctance was ascribed to an interest in protecting its assets there. But North Waziristan has also increasingly become home to the Pakistan army's most fearsome enemies. It is the base of Lashkar-e-Jhangvi, the sectarian terror group with deep links to al-Qaeda and the Pakistani Taliban, responsible for the slaughter of 94 Shi'ite Muslims in two days in two separate cities last week. And it is where some of the Pakistani Taliban's leaders from the Mehsud tribe skulk, afforded protection by Hafiz Gul Bahadur, a militant who also attacks U.S. and NATO troops across the border in Afghanistan, but enjoys the safe harbor of a non-aggression pact with the Pakistan Army. (Read more about the Waziristan offensive.)

The military official says that the army will have to wait for the right conditions to emerge before stirring the hornets' nest that North Waziristan has become. To take on any single group, the army would first try to isolate it, staving off resistance from the others. Collectively, the military official concedes, they pose too formidable a challenge now. But the worry is that by the time the army is ready to move, it may be too late.